메뉴 건너뛰기




Volumn 6, Issue 5, 2011, Pages

Selection and validation of reference genes for quantitative real-time PCR in buckwheat (Fagopyrum esculentum) based on transcriptome sequence data

Author keywords

[No Author keywords available]

Indexed keywords

CLATHRIN ADAPTER COMPLEX SUBUNIT FAMILY PROTEIN; F BOX PROTEIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; TIP41 LIKE PROTEIN; TRANSCRIPTOME; UBIQUITIN PROTEIN LIGASE 7; UNCLASSIFIED DRUG; VEGETABLE PROTEIN; PRIMER DNA;

EID: 79955940628     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019434     Document Type: Article
Times cited : (105)

References (38)
  • 1
    • 2442650370 scopus 로고    scopus 로고
    • The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
    • Vaucheret H, Vazquez F, Crété P, Bartel DP, (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18 (10): 1187-1197.
    • (2004) Genes Dev , vol.18 , Issue.10 , pp. 1187-1197
    • Vaucheret, H.1    Vazquez, F.2    Crété, P.3    Bartel, D.P.4
  • 2
    • 77952842148 scopus 로고    scopus 로고
    • Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box gene AGAMOUS-LIKE6
    • Koo SC, Bracko O, Park MS, Schwab R, Chun HJ, et al. (2010) Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box gene AGAMOUS-LIKE6. The Plant Journal 62: 807-816.
    • (2010) The Plant Journal , vol.62 , pp. 807-816
    • Koo, S.C.1    Bracko, O.2    Park, M.S.3    Schwab, R.4    Chun, H.J.5
  • 3
    • 77955666376 scopus 로고    scopus 로고
    • Functional analysis of the Arabidopsis PAL gene family in plant growth, development and response to environmental stress
    • Huang J, Gu M, Lai Z, Fan B, Shi K, et al. (2010) Functional analysis of the Arabidopsis PAL gene family in plant growth, development and response to environmental stress. Plant Physiology 153: 1526-1538.
    • (2010) Plant Physiology , vol.153 , pp. 1526-1538
    • Huang, J.1    Gu, M.2    Lai, Z.3    Fan, B.4    Shi, K.5
  • 4
    • 77954921218 scopus 로고    scopus 로고
    • ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis
    • Ren X, Chen Z, Liu Y, Zhang H, Zhang M, et al. (2010) ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. The Plant Journal 63 (3): 417-429.
    • (2010) The Plant Journal , vol.63 , Issue.3 , pp. 417-429
    • Ren, X.1    Chen, Z.2    Liu, Y.3    Zhang, H.4    Zhang, M.5
  • 5
    • 49949085913 scopus 로고    scopus 로고
    • Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus
    • Qiu JL, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, et al. (2008) Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus. EMBO J 27 (16): 2214-2221.
    • (2008) EMBO J , vol.27 , Issue.16 , pp. 2214-2221
    • Qiu, J.L.1    Fiil, B.K.2    Petersen, K.3    Nielsen, H.B.4    Botanga, C.J.5
  • 6
    • 77957890949 scopus 로고    scopus 로고
    • NmDef02, a novel antimicrobial gene isolated from Nicotiana megalosiphon confers high-level pathogen resistance under greenhouse and field conditions
    • Portieles R, Ayra C, Gonzalez E, Gallo A, Rodriguez R, et al. (2010) NmDef02, a novel antimicrobial gene isolated from Nicotiana megalosiphon confers high-level pathogen resistance under greenhouse and field conditions. Plant Biotechnol J 8 (6): 678-690.
    • (2010) Plant Biotechnol J , vol.8 , Issue.6 , pp. 678-690
    • Portieles, R.1    Ayra, C.2    Gonzalez, E.3    Gallo, A.4    Rodriguez, R.5
  • 7
    • 64149097786 scopus 로고    scopus 로고
    • The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    • Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55 (4): 611-22.
    • (2009) Clin Chem , vol.55 , Issue.4 , pp. 611-622
    • Bustin, S.A.1    Benes, V.2    Garson, J.A.3    Hellemans, J.4    Huggett, J.5
  • 8
    • 21344471138 scopus 로고    scopus 로고
    • Real-time RT-PCR normalisation; strategies and considerations
    • Huggett J, Dheda K, Bustin S, Zumla A, (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6 (4): 279-284.
    • (2005) Genes Immun , vol.6 , Issue.4 , pp. 279-284
    • Huggett, J.1    Dheda, K.2    Bustin, S.3    Zumla, A.4
  • 9
    • 32644481938 scopus 로고    scopus 로고
    • Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    • Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR, (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139 (1): 5-17.
    • (2005) Plant Physiol , vol.139 , Issue.1 , pp. 5-17
    • Czechowski, T.1    Stitt, M.2    Altmann, T.3    Udvardi, M.K.4    Scheible, W.R.5
  • 10
    • 47249141242 scopus 로고    scopus 로고
    • The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants
    • Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre JF, et al. (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J 6 pp. 609-618.
    • (2008) Plant Biotechnol J , Issue.6 , pp. 609-618
    • Gutierrez, L.1    Mauriat, M.2    Guénin, S.3    Pelloux, J.4    Lefebvre, J.F.5
  • 11
    • 77949820670 scopus 로고    scopus 로고
    • Buckwheat (Fagopyrum esculentum Moench) FeMT3 gene in heavy metal stress: protective role of the protein and inducibility of the promoter region under Cu(2+) and Cd(2+) treatments
    • Nikolić BD, Samardzić TJ, Bratić MA, Radin PI, Gavrilović PS, et al. (2010) Buckwheat (Fagopyrum esculentum Moench) FeMT3 gene in heavy metal stress: protective role of the protein and inducibility of the promoter region under Cu(2+) and Cd(2+) treatments. J Agric Food Chem 58 (6): 3488-94.
    • (2010) J Agric Food Chem , vol.58 , Issue.6 , pp. 3488-3494
    • Nikolić, B.D.1    Samardzić, T.J.2    Bratić, M.A.3    Radin, P.I.4    Gavrilović, P.S.5
  • 13
    • 78651337304 scopus 로고    scopus 로고
    • De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)
    • Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, et al. (2011) De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 12 (1): 30.
    • (2011) BMC Genomics , vol.12 , Issue.1 , pp. 30
    • Logacheva, M.D.1    Kasianov, A.S.2    Vinogradov, D.V.3    Samigullin, T.H.4    Gelfand, M.S.5
  • 14
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • research0034-research0034.11
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3 (7): research0034-research0034.11.
    • (2002) Genome Biol , vol.3 , Issue.7
    • Vandesompele, J.1    de Preter, K.2    Pattyn, F.3    Poppe, B.4    van Roy, N.5
  • 15
    • 3442876969 scopus 로고    scopus 로고
    • Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    • Andersen CL, Jensen JL, Ørntoft TF, (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64 (15): 5245-5250.
    • (2004) Cancer Res , vol.64 , Issue.15 , pp. 5245-5250
    • Andersen, C.L.1    Jensen, J.L.2    Ørntoft, T.F.3
  • 16
    • 1842483281 scopus 로고    scopus 로고
    • Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations
    • Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP, (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett 26 (6): 509-515.
    • (2004) Biotechnol Lett , vol.26 , Issue.6 , pp. 509-515
    • Pfaffl, M.W.1    Tichopad, A.2    Prgomet, C.3    Neuvians, T.P.4
  • 17
    • 33847643776 scopus 로고    scopus 로고
    • Quantification of mRNA using real-time RT-PCR
    • Nolan T, Hands RE, Bustin SA, (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1 (3): 1559-1582.
    • (2006) Nat Protoc , vol.1 , Issue.3 , pp. 1559-1582
    • Nolan, T.1    Hands, R.E.2    Bustin, S.A.3
  • 18
    • 79955943402 scopus 로고    scopus 로고
    • geNorm Software
    • geNorm Software [http://medgen.ugent.be/~jvdesomp/genorm/].
  • 19
    • 57049155443 scopus 로고    scopus 로고
    • Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR
    • Hong SY, Seo PJ, Yang MS, Xiang F, Park CM, (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol 8: 112.
    • (2008) BMC Plant Biol , vol.8 , pp. 112
    • Hong, S.Y.1    Seo, P.J.2    Yang, M.S.3    Xiang, F.4    Park, C.M.5
  • 20
    • 79959903517 scopus 로고    scopus 로고
    • Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR
    • Jarosová J, Kundu JK, (2010) Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR. BMC Plant Biol 10: 146.
    • (2010) BMC Plant Biol , vol.10 , pp. 146
    • Jarosová, J.1    Kundu, J.K.2
  • 21
    • 77950476641 scopus 로고    scopus 로고
    • Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida
    • Mallona I, Lischewski S, Weiss J, Hause B, Egea-Cortines M, (2010) Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biol 10: 4.
    • (2010) BMC Plant Biol , vol.10 , pp. 4
    • Mallona, I.1    Lischewski, S.2    Weiss, J.3    Hause, B.4    Egea-Cortines, M.5
  • 22
    • 43549088616 scopus 로고    scopus 로고
    • Arabidopsis UEV1D promotes Lysine-63-linked polyubiquitination and is involved in DNA damage response
    • Wen R, Torres-Acosta JA, Pastushok L, Lai X, Pelzer L, et al. (2008) Arabidopsis UEV1D promotes Lysine-63-linked polyubiquitination and is involved in DNA damage response. Plant Cell 20 (1): 213-27.
    • (2008) Plant Cell , vol.20 , Issue.1 , pp. 213-227
    • Wen, R.1    Torres-Acosta, J.A.2    Pastushok, L.3    Lai, X.4    Pelzer, L.5
  • 23
    • 75949111375 scopus 로고    scopus 로고
    • Arabidopsis deadenylases AtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses
    • Walley JW, Kelley DR, Nestorova G, Hirschberg DL, Dehesh K, (2010) Arabidopsis deadenylases AtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses. Plant Physiol 152 (2): 866-75.
    • (2010) Plant Physiol , vol.152 , Issue.2 , pp. 866-875
    • Walley, J.W.1    Kelley, D.R.2    Nestorova, G.3    Hirschberg, D.L.4    Dehesh, K.5
  • 24
    • 58549086530 scopus 로고    scopus 로고
    • Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process
    • Exposito-Rodriguez M, Borges A, Borges-Perez A, Perez J, (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8 (1): 131.
    • (2008) BMC Plant Biol , vol.8 , Issue.1 , pp. 131
    • Exposito-Rodriguez, M.1    Borges, A.2    Borges-Perez, A.3    Perez, J.4
  • 25
    • 77955093325 scopus 로고    scopus 로고
    • A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus
    • Chen X, Truksa M, Shah S, Weselake RJ, (2010) A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus. Anal Biochem 405 (1): 138-40.
    • (2010) Anal Biochem , vol.405 , Issue.1 , pp. 138-140
    • Chen, X.1    Truksa, M.2    Shah, S.3    Weselake, R.J.4
  • 26
    • 77649341683 scopus 로고    scopus 로고
    • Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree
    • Lin YL, Lai ZX, (2010) Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Plant Science 178: 359-365.
    • (2010) Plant Science , vol.178 , pp. 359-365
    • Lin, Y.L.1    Lai, Z.X.2
  • 27
  • 28
    • 78349297591 scopus 로고    scopus 로고
    • Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures
    • Desgagné-Penix I, Khan MF, Schriemer DC, Cram D, Nowak J, et al. (2010) Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures. BMC Plant Biol 10: 252.
    • (2010) BMC Plant Biol , vol.10 , pp. 252
    • Desgagné-Penix, I.1    Khan, M.F.2    Schriemer, D.C.3    Cram, D.4    Nowak, J.5
  • 29
    • 77957097203 scopus 로고    scopus 로고
    • Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes
    • Riggins CW, Peng Y, Stewart CN Jr, Tranel PJ, (2010) Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag Sci 66 (10): 1042-1052.
    • (2010) Pest Manag Sci , vol.66 , Issue.10 , pp. 1042-1052
    • Riggins, C.W.1    Peng, Y.2    Stewart Jr., C.N.3    Tranel, P.J.4
  • 30
    • 77956633353 scopus 로고    scopus 로고
    • Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill
    • de Almeida MR, Ruedell CM, Ricachenevsky FK, Sperotto RA, Pasquali G, et al. (2010) Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill. BMC Mol Biol 11: 73.
    • (2010) BMC Mol Biol , vol.11 , pp. 73
    • de Almeida, M.R.1    Ruedell, C.M.2    Ricachenevsky, F.K.3    Sperotto, R.A.4    Pasquali, G.5
  • 31
    • 64249143593 scopus 로고    scopus 로고
    • Transcript profiling of oilseed rape (Brassica napus) primed for biocontrol differentiate genes involved in microbial interactions with beneficial Bacillus amyloliquefaciens from pathogenic Botrytis cinerea
    • Sarosh BR, Danielsson J, Meijer J, (2009) Transcript profiling of oilseed rape (Brassica napus) primed for biocontrol differentiate genes involved in microbial interactions with beneficial Bacillus amyloliquefaciens from pathogenic Botrytis cinerea. Plant Mol Biol 70 (1-2): 31-45.
    • (2009) Plant Mol Biol , vol.70 , Issue.1-2 , pp. 31-45
    • Sarosh, B.R.1    Danielsson, J.2    Meijer, J.3
  • 32
    • 15944381065 scopus 로고    scopus 로고
    • Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication
    • Kim S, Yoo MJ, Albert VA, Farris JS, Soltis PS, et al. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Amer J Bot 91: 2102-2118.
    • (2004) Amer J Bot , vol.91 , pp. 2102-2118
    • Kim, S.1    Yoo, M.J.2    Albert, V.A.3    Farris, J.S.4    Soltis, P.S.5
  • 33
    • 0002594984 scopus 로고
    • A rapid DNA isolation from small amount of fresh leaf tissue
    • Doyle JJ, Doyle JL, (1987) A rapid DNA isolation from small amount of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
    • (1987) Phytochemical Bulletin , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 34
    • 79955932750 scopus 로고    scopus 로고
    • PrimerQuest
    • PrimerQuest [http://eu.idtdna.com/Scitools/Applications/Primerquest/default.aspx].
  • 35
    • 79955943324 scopus 로고    scopus 로고
    • OligoAnalyzer
    • OligoAnalyzer [http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer].
  • 36
    • 79955936517 scopus 로고    scopus 로고
    • Real-time PCR Miner
    • Real-time PCR Miner [http://www.miner.ewindup.info/version2].
  • 37
    • 27644482283 scopus 로고    scopus 로고
    • Comprehensive algorithm for quantitative real-time polymerase chain reaction
    • Zhao S, Fernald RD, (2005) Comprehensive algorithm for quantitative real-time polymerase chain reaction. J Comput Biol 12 (8): 1047-1064.
    • (2005) J Comput Biol , vol.12 , Issue.8 , pp. 1047-1064
    • Zhao, S.1    Fernald, R.D.2
  • 38
    • 38649136194 scopus 로고    scopus 로고
    • Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications
    • Mao F, Leung WY, Xin X, (2007) Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 7: 76.
    • (2007) BMC Biotechnol , vol.7 , pp. 76
    • Mao, F.1    Leung, W.Y.2    Xin, X.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.